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Research: Saturation mutagenesis reveals manifold determinants of exon definition
- Shengdong Ke,
- Vincent Anquetil,
- Jorge Rojas Zamalloa,
- Alisha Maity,
- Anthony Yang,
- Mauricio A. Arias,
- Sergey Kalachikov,
- James J. Russo,
- Jingyue Ju,
- and Lawrence A. Chasin
Genome Res. January 2018 28: 11-24; Published in Advance December 14, 2017, doi:10.1101/gr.219683.116
...molecules (Fig. 1B). Splicing of the WT exon takes place with an efficiency (percent spliced in, PSI; presented here as a proportion) of 0.065 (Ke et al. 2011); this low level is the result of depriving WT1-5 of its natural flanking intronic sequences (Zhang et al. 2005c). The modest splicing efficiency...
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Method: Quantitative evaluation of all hexamers as exonic splicing elements
- Shengdong Ke,
- Shulian Shang,
- Sergey M. Kalachikov,
- Irina Morozova,
- Lin Yu,
- James J. Russo,
- Jingyue Ju,
- and Lawrence A. Chasin
Genome Res. August 2011 21: 1360-1374; Published in Advance June 9, 2011, doi:10.1101/gr.119628.110
...successfully included the Figure 1. High-throughput definition of pre-mRNA splicing signals from sequence space. (A) The architecture of a linear minigene library. This minigene contains the Wilm’s tumor gene 1 exon 5 (WT1-5) as a central exon (yellow box) flanked by sequences from a Dhfr minigene (blue boxes...
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LETTER: Positive selection acting on splicing motifs reflects compensatory evolution
- Shengdong Ke,
- Xiang H.-F. Zhang,
- and Lawrence A. Chasin
Genome Res. April 2008 18: 533-543; Published in Advance January 18, 2008, doi:10.1101/gr.070268.107
...(see Methods) and aligned to the other primate s. As an estimate of neutral mutation rates, we enumerated changes in intron sequences. We ignored sequences located within 100 nt of exons, as these regions are known to harbor splicing regulatory signals ( Louie et al. 2003 ; Zhang et al. 2003 , 2005c...
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Letter: Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts
- Jeremy R. Sanford,
- Xin Wang,
- Matthew Mort,
- Natalia VanDuyn,
- David N. Cooper,
- Sean D. Mooney,
- Howard J. Edenberg,
- and Yunlong Liu
Genome Res. March 2009 19: 381-394; Published in Advance December 30, 2008, doi:10.1101/gr.082503.108
...corresponding to the canonical SFRS1 binding site. The consensus site was not only enriched in exons cross-linked to SFRS1 in vivo, but was also enriched in close proximity to splice sites. mRNAs encoding RNA processing factors were significantly overrepresented, suggesting that SFRS1 may broadly influence...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...annotated 3′ UTRs and 55 are not optimized for intronic regions (Xia et al. 2014; Gruber et al. 2018; Ha et al. 2018). 56 Detecting IPA poses additional challenges due to lower transcript abundance, complex splicing 57 patterns, and confounding signals from intron retention. While experimental methods...
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LETTER: A systematic analysis of intronic sequences downstream of 5′ splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation
- Isabel Aznarez,
- Yoseph Barash,
- Ofer Shai,
- David He,
- Julian Zielenski,
- Lap-Chee Tsui,
- John Parkinson,
- Brendan J. Frey,
- Johanna M. Rommens,
- and Benjamin J. Blencowe
Genome Res. August 2008 18: 1247-1258; Published in Advance May 2, 2008, doi:10.1101/gr.073155.107
...in the identification of G-rich motifs as part of dichotomous signals present in exon flanking sequences ( Zhang et al. 2005 ). U-rich sequences, however, have not been computationally analyzed or experimentally investigated on a large scale and therefore form the main focus of this article. Previous studies have shown...
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Methods: Ab initio identification of functionally interacting pairs of cis-regulatory elements
- Brad A. Friedman,
- Michael B. Stadler,
- Noam Shomron,
- Ye Ding,
- and Christopher B. Burge
Genome Res. October 2008 18: 1643-1651; Published in Advance September 17, 2008, doi:10.1101/gr.080085.108
...in introns flanking alternative “cassette” exons, suggesting a role in silencing of intervening exons, and we showed that these motifs can cooperatively silence splicing of an intervening exon in a splicing reporter assay. This approach can be easily generalized to problems beyond RNA splicing. Footnotes...
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LETTER: Genomic Characterization of Recent Human LINE-1 Insertions: Evidence Supporting Random Insertion
- Igor Ovchinnikov,
- Andrea B. Troxel,
- and Gary D. Swergold
Genome Res. December 1, 2001 11: 2050-2058; Published in Advance November 12, 2001, doi:10.1101/gr.194701
...exons ( Moran et al. 1999 ). The characteristics of an L1 insertion associated with a 3′ transduction is the presence of target site duplications surrounding both the L1 insertion and a segment of non-L1 3′ flanking DNA. Between the L1 and the transduced DNA resides the remnants of the poly(A) tail from...
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Research: CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer
- Hui Ling,
- Riccardo Spizzo,
- Yaser Atlasi,
- Milena Nicoloso,
- Masayoshi Shimizu,
- Roxana S. Redis,
- Naohiro Nishida,
- Roberta Gafà,
- Jian Song,
- Zhiyi Guo,
- Cristina Ivan,
- Elisa Barbarotto,
- Ingrid De Vries,
- Xinna Zhang,
- Manuela Ferracin,
- Mike Churchman,
- Janneke F. van Galen,
- Berna H. Beverloo,
- Maryam Shariati,
- Franziska Haderk,
- Marcos R. Estecio,
- Guillermo Garcia-Manero,
- Gijs A. Patijn,
- David C. Gotley,
- Vikas Bhardwaj,
- Imad Shureiqi,
- Subrata Sen,
- Asha S. Multani,
- James Welsh,
- Ken Yamamoto,
- Itsuki Taniguchi,
- Min-Ae Song,
- Steven Gallinger,
- Graham Casey,
- Stephen N. Thibodeau,
- Loïc Le Marchand,
- Maarit Tiirikainen,
- Sendurai A. Mani,
- Wei Zhang,
- Ramana V. Davuluri,
- Koshi Mimori,
- Masaki Mori,
- Anieta M. Sieuwerts,
- John W.M. Martens,
- Ian Tomlinson,
- Massimo Negrini,
- Ioana Berindan-Neagoe,
- John A. Foekens,
- Stanley R. Hamilton,
- Giovanni Lanza,
- Scott Kopetz,
- Riccardo Fodde,
- and George A. Calin
Genome Res. September 2013 23: 1446-1461; Published in Advance June 24, 2013, doi:10.1101/gr.152942.112
..., miR–17–5p, and miR–20a are up-regulated by CCAT2 through TCF7L2-mediated transcriptional regulation. We further identify the physical interaction between CCAT2 and TCF7L2 resulting in an enhancement of WNT signaling activity. We show that CCAT2 is itself a WNT downstream target, which suggests...
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RESOURCE: Complete MHC Haplotype Sequencing for Common Disease Gene Mapping
- C. Andrew Stewart,
- Roger Horton,
- Richard J.N. Allcock,
- Jennifer L. Ashurst,
- Alexey M. Atrazhev,
- Penny Coggill,
- Ian Dunham,
- Simon Forbes,
- Karen Halls,
- Joanna M.M. Howson,
- Sean J. Humphray,
- Sarah Hunt,
- Andrew J. Mungall,
- Kazutoyo Osoegawa,
- Sophie Palmer,
- Anne N. Roberts,
- Jane Rogers,
- Sarah Sims,
- Yu Wang,
- Laurens G. Wilming,
- John F. Elliott,
- Pieter J. de Jong,
- Stephen Sawcer,
- John A. Todd,
- John Trowsdale,
- and Stephan Beck
Genome Res. June 2004 14: 1176-1187; Published in Advance May 12, 2004, doi:10.1101/gr.2188104
...-associated-haplotypes HLA-A3-B7-Cw7-DR15 and HLA-A1-B8-Cw7-DR3 were sequenced in their entirety through a bacterial artificial chromosome (BAC) cloning strategy using the consanguineous cell lines PGF and COX, respectively. The two sequences were annotated to encompass all described splice variants of expressed genes...

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